التفاصيل البيبلوغرافية
| العنوان: |
nf-core/eager: [2.4.0] - 20201-09-14 |
| المؤلفون: |
James A. Fellows Yates, Alexander Peltzer, Thiseas C. Lamnidis, Maxime Borry, ZandraFagernas, Ido Bar, Aida Andrades Valtueña, alexandregilardet, nf-core bot, Maxime U. Garcia, Evan Floden, Phil Ewels, Patrick Hüther, Charles Plessy, Gisela Gabernet, sc13-bioinf, Åshild J. Vågene, Harshil Patel, Olga Botvinnik, Selina Carlhoff, Alex Hübner |
| بيانات النشر: |
Zenodo |
| سنة النشر: |
2021 |
| المجموعة: |
Zenodo |
| الوصف: |
Added #317 Added bcftools stats for general genotyping statistics of VCF files #651 - Adds removal of adapters specified in an AdapterRemoval adapter list file #642 and #431 adds post-adapter removal barcode/fastq trimming #769 - Adds lc_extrap mode to preseq (suggested by @roberta-davidson) Fixed Fixed some missing or incorrectly reported software versions #771 Remove legacy code Improved output documentation for MultiQC general stats table (thanks to @KathrinNaegele and @esalmela) Improved output documentation for BowTie2 (thanks to @isinaltinkaya) #612 Updated BAM trimming defaults to 0 to ensure no unwanted trimming when mixing half-UDG with no-UDG (thanks to @scarlhoff) #722 Updated BWA mapping mapping parameters to latest recommendations - primarily alnn back to 0.01 and alno to 2 as per Oliva et al. 2021 (10.1093/bib/bbab076) Updated workflow diagrams to reflect latest functionality #787 Adds memory specification flags for the GATK UnifiedGenotyper and HaplotyperCaller steps (thanks to @nylander) Fixed issue where MultiVCFAnalyzer would not pick up newly generated VCF files, when specifying additional VCF files. #790 Fixed kraken2 report file-name collision when sample names have . in them #792 Fixed java error messages for AdapterRemovalFixPrefix being hidden in output #794 Aligned default test profile with nf-core standards (test_tsv is now test) Dependencies Bumped python: 3.7.3 -> 3.9.4 Bumped markdown: 3.2.2 -> 3.3.4 Bumped pymdown-extensions: 7.1 -> 8.2 Bumped pyments: 2.6.1 -> 2.9.0 Bumped adapterremoval: 2.3.1 -> 2.3.2 Bumped picard: 2.22.9 -> 2.26.0 Bumped samtools 1.9 -> 1.12 Bumped angsd: 0.933 -> 0.935 Bumped gatk4: 4.1.7.0 -> 4.2.0.0 Bumped multiqc: 1.10.1 -> 1.11 Bumped bedtools 2.29.2 -> 2.30.0 Bumped libiconv: 1.15 -> 1.16 Bumped preseq: 2.0.3 -> 3.1.2 Bumped bamutil: 1.0.14 -> 1.0.15 Bumped pysam: ... |
| نوع الوثيقة: |
other/unknown material |
| اللغة: |
unknown |
| Relation: |
https://github.com/nf-core/eager/tree/2.4.0; https://doi.org/10.5281/zenodo.1465061; https://doi.org/10.5281/zenodo.5507524; oai:zenodo.org:5507524 |
| DOI: |
10.5281/zenodo.5507524 |
| الاتاحة: |
https://doi.org/10.5281/zenodo.5507524 |
| Rights: |
info:eu-repo/semantics/openAccess ; Other (Open) |
| رقم الانضمام: |
edsbas.DC06E2C8 |
| قاعدة البيانات: |
BASE |